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PubMed1975

Fine structural localization of alkaline phosphatase in the granular pneumonocytes of hamster lung.

The fine structural localization of nonspecific alkaline phosphatase was studied in the granular pneumonocytes (type II alveolar epithelial cells) of hamster lung by incubating sections of glutaraldehyde-fixed tissues in a medium containing lead ions and sodium beta-glycerophosphate or alpha-naphthyl acid phosphate. The specificity of the reaction was tested by exposing the sections to inhibitors of alkaline phosphatase. The results showed that alkaline phosphatase activity was present in the inclusion bodies of granular pneumonocytes. The enzyme reaction was strong in the membrane lining the inclusion bodies and a weaker reaction was generally detectable in the inclusion contents. Although only a proportion of the inclusion bodies showed enzyme activity, there was no obvious correlation between the reactivity of the inclusions and their intracellular position or size. The other organelles were unreactive. The finding of alkaline phosphatase activity within the inclusion bodies of granular pneumonocytes is an enigma as these organelles are generally considered to be lyosomes.

Alkaline Phosphatase↗
PubMed2005

Bound site of Mo atoms and its local structure in a Mo/HY catalyst characterized by extended X-ray absorption fine structure and density functional calculation.

The bound site of Mo atoms and its local structure in a Mo/HY catalyst have been determined by detailed analysis of extended X-ray absorption fine structure (EXAFS). Molybdenum was introduced in the supercage of HY zeolite by cycles of saturated adsorption of Mo(CO)6 at room temperature and subsequent thermal decomposition at 573 K. Two Mo atoms per supercage were immobilized in each CVD-thermal treatment cycle. The Mo loading increased linearly with the cycles up to three cycles at saturation, where six Mo atoms were supported. Temperature-programmed decomposition of the adsorbed Mo(CO)6 was also characterized by GC, QMS, and FT-IR, respectively. The EXAFS analysis including multiple scattering based on theoretical calculations revealed that Mo bound with two oxygen atoms connects to Al, where one of the two oxygen atoms had been associated with a proton. The bound site is called the S(III)' site. The zeolite framework was significantly distorted by the introduction of low-valent Mo, resulting in isolation of the [MoO2Al] unit from the surrounding zeolite framework due to a quasi-disruption of Si-O bonds adjacent to the unit. In the mild oxidation of the low-valent Mo/HY sample two Mo=O bonds were newly formed and the position of Mo was displaced by 0.06 nm so that the distortion of zeolite framework around the Al atom was relieved. The structures were also supported by DFT calculations. This study is the first example that the position of metal cation in zeolite was determined unambiguously by the EXAFS analysis.

Journal Article↗
PubMed2000

Role of pump diffraction on the stability of localized structures in degenerate optical parametric oscillators.

We show that the stability range of localized structures (LS's) in the form of minimum size phase domains in degenerate optical parametric oscillators is enhanced by increasing the diffraction of the pump wave. Pump diffraction enhances spatial oscillations of decaying tails of domain boundaries, whereas spatially oscillating (weakly decaying) tails prevent the collapse of LS's, enhance their stability range, and allow the existence of more complex LS's in the form of molecules.

Journal Article↗
PubMed2002

Tailoring the profile and interactions of optical localized structures.

We experimentally demonstrate the broad tunability of the main features of optical localized structures (LS's) in a nonlinear interferometer. By discussing how a single LS depends on the system spatial frequency bandwidth, we show that a modification of its tail leads to the possibility of tuning the interactions between LS pairs, and thus the equilibrium distances at which LS bound states form. This is in agreement with a general theoretical model describing weak interactions of LS in nonlinear dissipative systems.

Journal Article↗
PubMed2001

Local structure of liquid and solid silver halides probed by XAFS.

Investigation of the local structure of the high-temperature liquid and solid phases in the 300-725 K range of AgBr has been performed using the x-ray absorption spectroscopy (XAS). Structural results are compared with existing diffraction studies and computer simulations demonstrating the reliability of the XAS technique in determining the short-range structure. Present results on solid AgBr are in agreement with known thermal expansion data. The short-range g(r) of liquid AgBr is reconstructed showing the unique insight provided by the XAS technique in measuring short-range atom-atom correlations in liquids.

Journal Article↗
PubMed2005

Two classes of 5S rDNA unit arrays of the silver fir, Abies alba Mill.: structure, localization and evolution.

The structure and organization of the 5S ribosomal DNA units of the silver fir, Abies alba Mill., as well as their position in the chromosome complement were investigated. PCR amplification of the gene and nontranscribed spacer region, sequence analysis and Southern hybridization, using a homologous probe, detected DNA sequences of approximately 550 bp and 700 bp. Sequence analysis of the spacers revealed that the difference in length between the sequences occurred in the middle spacer region as a result of the amplification of a 75-bp sequence of the short unit class, which is organized in four 54- to 68-bp tandem repeats in the long spacer unit. The 5S rDNA transcribed region is 120 bp long and shows high sequence similarity with other gymnosperm species. The comparative analysis of 5' and 3' flanking sequences of 5S rRNA genes of silver fir and other gymnosperms indicates that A. alba spacer units have the same rate of evolution and are more closely related to Larix and Pseudotsuga than to Pinus and Picea. Southern hybridization and fluorescence in situ hybridization of metaphase chromosomes of A. alba suggest that the short and long spacer units are organized as separate tandem arrays at two chromosomal loci on chromosomes V and XI.

Abies↗
PubMed2002

Local structural properties of the V3 loop of Thailand HIV-1 isolate.

The model of locally accurate conformation for the HIV-Thailand principal neutralizing determinant (PND) located within the V3 loop of the virus envelope protein gp120 was built in terms of NMR spectroscopy data. To this end, the NMR-based conformational analysis of synthetic molecule representing the peptide copy of the fragment under study was carried out using the published sequential d connectivity data and values of spin-spin coupling constants. As a result, (i) the local structure for the V3 loop from Thailand isolate was determined, (ii) the conformations of its irregular segments were analyzed, and the secondary structure elements identified, (iii) the ensemble of conformers matching the experimental and theoretical data was derived for the stretch forming the neutralizing epitope of the HIV-Thailand PND, (iv) to estimate the probability of realizing each of these conformers in solution, the results obtained were collated with the X-ray data for corresponding segments in synthetic molecules imitating the central region of the HIV-MN PND as well as for homologous segments 39-44 in Bence-Jonce REI protein (BJRP), 41-46 in immunoglobulin lambda (Ig lambda), and 50-55 in beta-chain of horse hemoglobin (HH), (v) to find the conserved structural motifs inside diverse HIV-1 isolates, the structure determined was compared with the one derived earlier for the HIV-MN PND from NMR spectroscopy data, (vi) on the basis of all data obtained, the 3D structure model describing the set of biologically relevant conformations, which may present different antigenic determinants to the immune system in various HIV-1 isolates, was proposed for the immunogenic crown of the V3 loop. The results obtained are discussed in conjunction with the data on the structure for the HIV-1 PND reported in literature.

Amino Acid Sequence↗
PubMed2005

Quantitative local structure refinement from XANES: multi-dimensional interpolation approach.

A new method to determine local structure in terms of a few structural parameters is proposed and realised in FitIt software. It is based on fitting of X-ray absorption near-edge structure (XANES) spectra using the combination of full multiple-scattering calculations, and multi-dimensional interpolation of spectra as a function of structural parameters. The procedure is divided into two steps: the construction of an interpolation polynomial, and the fitting of experimental spectra using the interpolation polynomial. During the construction of the polynomial, multiple-scattering calculations for certain sets of structural parameters are needed. The strategy for the selection of the most important expansion terms and corresponding sets of structural parameters is proposed. Fitting of the spectrum using multi-dimensional interpolation is very fast (a few seconds) because multiple-scattering calculations are unnecessary during this step. Also, this approach allows the development of a visual interface with the possibility of seeing the spectrum that corresponds to any set of structural parameters immediately. Thus, using a very limited number of multiple-scattering calculations, which are most time-consuming, it is possible to fit XANES. The interpolation polynomial construction procedure for three model molecules, FeS4, FeO6 and Ni(CN)4, is demonstrated. An additional test has been performed for the latter most-complex example to check the assumption that a minimum of discrepancy between theoretical and experimental spectra corresponds only to the correct structure of the complex. A comparison with another XANES fitting software, MXAN, is given.

Algorithms↗
PubMed2006

Pattern formation and localized structures in reaction-diffusion systems with non-Fickian transport.

We study the robust dynamical behaviors of reaction-diffusion systems where the transport gives rise to non-Fickian diffusion. A prototype model describing the deposition of molecules in a surface is used to show the generic appearance of Turing structures which can coexist with homogeneous states giving rise to localized structures through the pinning mechanism. The characteristic lengths of these structures are in the nanometer region in agreement with recent experimental observations.

Journal Article↗
PubMed1991

Alternating zinc fingers in the human male-associated protein ZFY: HX3H and HX4H motifs encode a local structural switch.

The two-finger repeat in the human male-associated protein ZFY provides a model for comparative 2D-NMR studies of classical and variant Zn fingers. This repeat is defined in part by an alternation in spacing between consensus (HX3H) and variant (HX4H) histidine spacings. To investigate the effects of a "switch" between alternative histidine spacings, we have designed an HX3H analogue of a representative HX4H domain of known structure [ZFY-6; Kochoyan, M., Havel, T., Nguyen, D. T., Dahl, C. E., Keutmann, H. T., & Weiss, M. A. (1991) Biochemistry 30, 3371-3386]. The HX3H analogue (designated ZFY-switch) forms a tetrahedral Co2+ complex whose thermodynamic stability is similar to that of the parent peptide. 2D-NMR studies demonstrate that ZFY-switch and ZFY-6, although similar in overall structure, exhibit significant local changes near the site of deletion. Whereas the HX4H site in the native finger forms a nonstandard loop, the HX3H site in ZFY-switch folds as a 3(10) extension of the C-terminal alpha-helix, as observed in the NMR solution structure of a consensus HX3H domain [Lee, M. S., Gippert, G. P., Soman, K. V., Case, D. A., & Wright, P. E. (1989) Science 245, 635-637] and in the crystal structure of a representative Zn finger-DNA complex [Pavletich, N. P., & Pabo, C. O. (1991) Science 252, 809-817]. We propose that variant histidine spacings (HX3H and HX4H) encode a local switch between alternative surface architectures with implications for models of protein-DNA recognition.

Amino Acid Sequence↗
PubMed2000

Localized structures in nonlinear lattices with diffusive coupling and external driving

We study the stabilization of localized structures by discreteness in one-dimensional lattices of diffusively coupled nonlinear sites. We find that in an external driving field these structures may lose their stability by either relaxing to a homogeneous state or nucleating a pair of oppositely moving fronts. The corresponding bifurcation diagram demonstrates a cusp singularity. The obtained analytic results are in good quantitative agreement with numerical simulations.

Journal Article↗
PubMed1999

Localized structural effects of electrostatic interactions in a thermostable enzyme.

The sequence and resolved structure of thermotrophic isopropylmalate dehydrogenase (IPMDH) and a related protein, mesotrophic isocitrate dehydrogenase (IDH), were compared emphasizing clusters of charged residues identified from X-ray crystallographic studies (Wallon, G., Kryger, G., Lovett, S. T., Oshima, T., Ringe, D., and Petsko, G. A. (1997) J. Mol. Biol. 266, 1016-1031). Mesotrophic isocitrate dehydrogenase was used for comparison because crystallographic data for a mesotrophic form of IPMDH was not available in the database. The structural features in the region of these clusters were compared and localized conformational differences were found in the thermotroph compared to the mesotroph. Because the overall topology of the two proteins is similar, it was concluded that these localized structural differences induced by electrostatic interactions between charged residues in the thermotrophic enzyme were responsible for the enhanced thermal stability of proteins from thermotroph.

3-Isopropylmalate Dehydrogenase↗
PubMed2000

Local Structure Analysis of Strontium Sorption to Hydrous Manganese Oxide.

To develop mechanistic models of contaminant distribution processes, we conducted an X-ray absorption fine structure analysis of strontium sorption to hydrous manganese oxide (HMO). Sr K-edge measurements were performed at 298, 220, and 77 K, and at sample loadings from 10(-4) to 10(-2) mol Sr/g HMO. Results from fitting the first shell in the sorbed samples indicate that strontium is surrounded by 10-12 oxygen atoms at an average distance of 2.58 Å. This coordination environment is consistent with the strontium atom remaining hydrated upon sorption to the oxide, where in water hydrated strontium has approximately 9 atoms of oxygen at 2.62 Å. Furthermore, the temperature dependence of the strontium-oxygen bond also suggests physical adsorption due to the large contribution of the dynamic component of the Debye Waller factor. Although second-shell data are consistent with either 3 manganese atoms at 4.12 Å or 6 strontium atoms at 3.88 Å, both the near-edge and fine structure data for the manganese K-edge indicate that the local coordination environment of the manganese ion remains intact as a function of time or strontium sorption. Furthermore, the local structure of amorphous manganese oxide is highly ordered. Copyright 2000 Academic Press.

Journal Article↗
PubMed1990

Automatic definition of recurrent local structure motifs in proteins.

An automatic procedure for defining recurrent folding motifs in proteins of known structure is described. These motifs are formed by short polypeptide fragments of equal size containing between four and seven residues. The method applies a classical clustering algorithm that operates on distances between selected backbone atoms. In one application, we use it to cluster all protein fragments into only four structural classes. This classification is rough considering the observed diversity of local structures, but comparable in homogeneity to the four classes of secondary structure (alpha-helix, beta-strand, turn and coil). Yet, it discriminates between extended and curved coil and distinguishes beta-bulges from beta-strands. In a second application, the clustering procedure is combined with assignment of backbone dihedral angles to allowed regions in the Ramachandran map. This produces an exhaustive repertoire of highly homogeneous families of structural motifs that contains all the beta-hairpins, beta alpha- and alpha beta-loops previously defined by manual procedures, and new structural families of which two examples, a beta alpha-loop and an alpha-helix beginning, are analyzed in detail. The described automatic procedures should be useful in categorizing structure information in proteins, thereby increasing our ability to analyze relations between structure and sequence.

Amino Acid Sequence↗
PubMed1979

Fine structural localization of thiamine pyrophosphatase and acid phosphatase activities in the mouse pancreatic acinar cell.

The fine structural localization of thiamine pyrophosphatase (TPPase) and acid phosphatase (AcPase) was examined in pancreatic acinar cells of fasting and fed mice. The results were not affected by these conditions. TPPase activity was positive in two and sometimes three cisternae of the inner Golgi lamellae as well as in the condensing vacuoles of the trans area, but negative in the rigid lamellae and small vesicles of the trans area. AcPase activity was demonstrated in two and sometimes three cisternae of inner Golgi lamellae, condensing vacuoles, rigid lamellae, lysosomes and smooth or coated vesicles in the trans area. The inner Golgi lamellae and the condensing vacuoles were positive for both enzyme activities. From these facts, the lysosome is considered to be formed not only in the GERL system but also through the rough endoplasmic reticulum-Golgi apparatus route. It is reasonable to consider that Novikoff's GERL is not independent from the Golgi apparatus but represents a part of this organelle.

Acid Phosphatase↗
PubMed1993

Changes in global stability and local structure of cytochrome c upon substituting phenylalanine-82 with tyrosine.

We have examined the F82Y;C102T variant of Saccharomyces cerevisiae iso-1-cytochrome c using high-resolution proton nuclear magnetic resonance spectroscopy, chemical denaturation, and differential scanning calorimetry. Comparison of proton chemical shifts, paramagnetic shifts, and nuclear Overhauser effects indicates structural changes are localized to the vicinity of position 82. One alteration involves the rearrangement of the side chain of leucine-85. Using many more proton assignments than were available in the initial report [G. J. Pielak, R. A. Atkinson, J. Boyd, and R. J. P. Williams, Eur. J. Biochem. 177, 179-185 (1988)], a second alteration involving an interaction between arginine-13 and tyrosine-82 is observed. The interaction appears to involve a hydrogen bond with the eta-protons of arginine's guanido group acting as donor and tyrosine's phenolic eta-oxygen as acceptor. In spite of this potentially-stabilizing interaction, the free energy of denaturation decreases by approximately 2.4 kcal mol-1. Results are discussed with respect to alterations in the native and denatured states.

Cytochrome c Group↗
PubMed2003

Protein local structure prediction from sequence.

A basis set of protein canonical fragments, or centroids, represents the range of local structure found in globular proteins. We develop a methodology to predict centroids from the amino acid sequence. The predictor gives the probability of each centroid in the basis set, at each loci along the backbone. The predictor selects the best-fit centroid at about 40% of the loci. The predicted probabilities are accurate and can be used to judge the confidence of each centroid prediction. For example, when filtering out centroids with <0.50 probability, the predictor is 65% accurate, although such high-probability centroids occur at only 28% of the loci. Centroids with high probability can be interpreted as segments that are highly influenced by the amino acid sequence, whereas centroids with low probability can be interpreted as segments that are more likely influenced by tertiary contacts. Low-resolution, starting point structures, can be generated by fitting the predicted centroids together.

Animals↗
PubMed1971

Fine structural localization of acyltransferases. The monoglyceride and -glycerophosphate pathways in intestinal absorptive cells.

A study of the fine structural localization of the acyltransferases of the monoglyceride and alpha-glycerophosphate pathways for triglyceride synthesis in the intestinal absorptive cell is reported. Glutaraldehyde-fixed tissue was found to synthesize diglyceride and triglyceride from monopalmitin and palmityl CoA, and parallel morphological studies showed the appearance of lipid droplets in the smooth endoplasmic reticulum of the absorptive cell. Glutaraldehyde-fixed tissue also synthesized triglyceride from alpha-glycerophosphate, although this enzyme system was more susceptible to fixation than the monoglyceride pathway acyltransferases. Cytochemical methods for the localization of free CoA were based (a) on the formation of the insoluble lanthanium mercaptide of CoA and (b) on the reduction of ferricyanide by CoA to yield ferrocyanide which forms an insoluble precipitate with manganous ions. By these methods the monoglyceride pathway acyltransferases were found to be located mainly on the inner surface of the smooth endoplasmic reticulum. The alpha-glycerophosphate pathway acyltransferases were localized mainly on the rough endoplasmic reticulum. Activity limited to the outer cisternae of the Golgi membranes occurred with both pathways. The possible organization of triglyceride absorption and chylomicron synthesis is discussed in view of these results.

Absorption↗